Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Temperature upshift in E coli gyrBT strain, time series

ABSTRACT: Responses of Escherichia coli W3110gyrb234 as they are upshifted to 42C Escherichia coli W3110gyrb234 cells sampled at several time points (2,5, 10, 40 min) as they are shifted to 42 C in LB, vs 0 min before upshift in LB

ORGANISM(S): Escherichia coli

SUBMITTER: Arkady Khodursky

PROVIDER: E-GEOD-4417 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

A classification based framework for quantitative description of large-scale microarray data.

Sangurdekar Dipen P DP Srienc Friedrich F Khodursky Arkady B AB

Genome biology 20060420 4

Genome-wide surveys of transcription depend on gene classifications for the purpose of data interpretation. We propose a new information-theoretical-based method to: assess significance of co-expression within any gene group; quantitatively describe condition-specific gene-class activity; and systematically evaluate conditions in terms of gene-class activity. We applied this technique to describe microarray data tracking Escherichia coli transcriptional responses to more than 30 chemical and phy ...[more]

PMID: 16626502

Similar Datasets

Temperature upshift in E coli gyrBT strain, time series

Project description:Responses of Escherichia coli W3110gyrb234 as they are upshifted to 42C Keywords: time course

2006-03-09 | GSE4417 | GEO

Ecoli DH5alpha, pUC overexpression in LB + Amp vs no pUC

Project description:Responses of Escherichia coli DH5alpha as they overexpress pUC at different ODs in LB + Amp Escherichia coli DH5alpha expressing pUC sampled at different ODs (0.2, 0.5, 0.9) in LB + Amp vs cells not producing pUC

2010-07-01 | E-GEOD-4379 | biostudies-arrayexpress

Transcriptome analysis of Escherichia coli O157:H7 EDL933 during rumen fluid exposure using microarrays

2010-12-01 | GSE16747 | GEO

Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock using microarrays

2009-04-01 | GSE11463 | GEO

Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate

Project description:Sodium benzoate is a widely used food antimicrobial in drinks and fruit juices. A microarray study was conducted to determine the transcriptional response of Escherichia coli O157:H7 to 0.5% (w/v) sodium benzoate. Stationary phase E. coli O157:H7 grown in 150 ml Luria-Bertani broth (LB) was exposed to 0 (control) and 0.5% sodium benzoate. Each treatment was duplicated and sampled at 0 (immediately after exposure), 5, 15, 30, and 60 min. Total RNA was extracted and analyzed with E. coli 2.0 Gene Chips.

2009-10-05 | GSE17519 | GEO

Stationary phase in LB, genomic DNA reference

Project description:Responses of Escherichia coli MG1655 in stationary phase in LB Keywords: time course

2006-03-08 | GSE4380 | GEO

Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock using microarrays

Project description:The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of heat shock on E. coli O157:H7, global transcript levels of strain EDL933 cells shifted from 37°C to 50°C for 15 min were compared to cells left at 37°C using microarrays. Keywords: Stress Response Twelve independent RNA samples from heat shocked cultures were paired with twelve independent RNA samples from control cultures for hybridization to twelve two-color microarrays. For six arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other six arrays to overcome dye bias.

2009-04-01 | E-GEOD-11463 | biostudies-arrayexpress

Ecoli DH5alpha, pUC overexpression in LB + Amp vs no pUC

Project description:Responses of Escherichia coli DH5alpha as they overexpress pUC at different ODs in LB + Amp Keywords: time course

2006-03-08 | GSE4379 | GEO

Novobiocin treatment in LB

Project description:Responses of Escherichia coli at 5 mins as they are treated to different concentrations of Novobiocin in LB Keywords: dosage course

2006-03-08 | GSE4378 | GEO

Transcriptome analysis of Escherichia coli O157:H7 EDL933 during rumen fluid exposure using microarrays

Project description:The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of rumen fluid on E. coli O157:H7, global transcript levels of strain EDL933 cells resuspended in heat clarified rumen fluid for 15 min were compared to cells resuspended in fresh LB using microarrays. Seven independent RNA samples from rumen fluid treated cultures were paired with seven independent RNA samples from control cultures for hybridization to seven two-color microarrays. For three arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other four arrays to overcome dye bias.

2010-12-01 | E-GEOD-16747 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data